plotManhattan {Sushi} | R Documentation |
plots a Manhattan plot
plotManhattan(bedfile, chrom = NULL, chromstart = NULL, chromend = NULL, pvalues, genome = NULL, col = SushiColors(5), space = 0.01, ymax = 1.04, ...)
bedfile |
bedfile for Manhattan plot |
chrom |
chromosome of region to be plotted |
chromstart |
start position |
chromend |
end position |
pvalues |
pvalues to be used for plotting (will be converted to -log(10) space) |
genome |
A genome object (2 columns: column 1 = chromosome name, column 2 = length of chromosome). Required if plotting multiple chromosomes at once. |
col |
single colors, vector of colors, or color palette for coloring points |
space |
the space in between each chromosome as a fraction of the width of the plot |
ymax |
fraction of max y value to set as height of plot. |
... |
Arguments to be passed to methods such as |
data(Sushi_GWAS.bed) data(Sushi_hg18_genome) chrom1 = "chr11" chromstart1 = 500000 chromend1 = 5050000 plotManhattan(bedfile=Sushi_GWAS.bed,pvalues=Sushi_GWAS.bed[,5],genome=Sushi_hg18_genome,col=topo.colors,cex=0.75) labelgenome(genome=Sushi_hg18_genome,side=1,scipen=20,n=4,scale="Mb",edgeblankfraction=0.20,line=.18,chromline=.5,scaleline=0.5) axis(side=2,las=2,tcl=.2) mtext("log10(P)",side=2,line=1.75,cex=.75,font=2)